Hydrophilic interaction chromatography (HILIC) liquid chromatography/mass spectrometry (LC/MS) is appropriate for all native and reductively aminated glycan classes. HILIC carries the advantage that retention times (RTs) vary predictably according to oligosaccharide composition. Chromatographic conditions are compatible with sensitive and reproducible glycomics analysis of large numbers of samples. The data are extremely useful for quantitative profiling of glycans expressed in biological tissues. With these analytical developments, the rate limiting factor for widespread use of HILIC LC/MS in glycomics is the analysis of the data. In order to eliminate this problem, a Java-based open source software tool, Manatee, was developed for targeted analysis of HILIC LC/MS glycan data sets. This tool uses user-defined lists of compositions that specify the glycan chemical space in a given biological context. The program accepts high resolution LC/MS data using the public mzXML format and is capable of processing a large data file in a few minutes on a standard desktop computer. The program allows mining of HILIC LC/MS data with an output compatible with multivariate statistical analysis. It is envisaged that the Manatee tool will complement more computationally intensive LC/MS processing tools based on deconvolution and deisotoping of LC/MS data. The capabilities of the tool were demonstrated using a set of HILIC LC/MS data on organ-specific heparan sulfates.

DNA adducts, which block replicative DNA polymerases (DNAPs), are often bypassed by lesion-bypass DNAPs, which are mostly in the Y-Family. Y-Family DNAPs can do non-mutagenic or mutagenic dNTP insertion, and understanding this difference is important, because mutations transform normal into tumorigenic cells. Y-Family DNAP architecture that dictates mechanism, as revealed in structural and modeling studies, is considered. Steps from adduct blockage of replicative DNAPs, to bypass by a lesion-bypass DNAP, to resumption of synthesis by a replicative DNAP are described. Catalytic steps and protein conformational changes are considered. One adduct is analyzed in greater detail: the major benzo[a]pyrene adduct (B[a]P-N2-dG), which is bypassed non-mutagenically (dCTP insertion) by Y-family DNAPs in the IV/κ-class and mutagenically (dATP insertion) by V/η-class Y-Family DNAPs. Important architectural differences between IV/κ-class versus V/η-class DNAPs are discussed, including insights gained by analyzing ~400 sequences each for bacterial DNAPs IV and V, along with sequences from eukaryotic DNAPs kappa, eta and iota. The little finger domains of Y-Family DNAPs do not show sequence conservation; however, their structures are remarkably similar due to the presence of a core of hydrophobic amino acids, whose exact identity is less important than the hydrophobic amino acid spacing.

System-level metabolic network models enable the computation of growth and metabolic phenotypes from an organism’s genome. In particular, flux balance approaches have been used to estimate the contribution of individual metabolic genes to organismal fitness, offering the opportunity to test whether such contributions carry information about the evolutionary pressure on the corresponding genes. Previous failure to identify the expected negative correlation between such computed gene-loss cost and sequence-derived evolutionary rates in Saccharomyces cerevisiae has been ascribed to a real biological gap between a gene’s fitness contribution to an organism “here and now” and the same gene’s historical importance as evidenced by its accumulated mutations over millions of years of evolution. Here we show that this negative correlation does exist, and can be exposed by revisiting a broadly employed assumption of flux balance models. In particular, we introduce a new metric that we call “function-loss cost”, which estimates the cost of a gene loss event as the total potential functional impairment caused by that loss. This new metric displays significant negative correlation with evolutionary rate, across several thousand minimal environments. We demonstrate that the improvement gained using function-loss cost over gene-loss cost is explained by replacing the base assumption that isoenzymes provide unlimited capacity for backup with the assumption that isoenzymes are completely non-redundant. We further show that this change of the assumption regarding isoenzymes increases the recall of epistatic interactions predicted by the flux balance model at the cost of a reduction in the precision of the predictions. In addition to suggesting that the gene-to-reaction mapping in genome-scale flux balance models should be used with caution, our analysis provides new evidence that evolutionary gene importance captures much more than strict essentiality.

Understanding how genetic modifications, individual or in combinations, affect phenotypes is a challenge common to several areas of biology, including human genetics, metabolic engineering, and evolutionary biology. Much of the complexity of how genetic modifications produce phenotypic outcomes has to do with the lack of independence, or epistasis, between different perturbations: the phenotypic effect of one perturbation depends, in general, on the genetic background of previously accumulated modifications, i.e., on the network of interactions with other perturbations. In recent years, an increasing number of high-throughput efforts, both experimental and computational, have focused on trying to unravel these genetic interaction networks. Here we provide an overview of how systems biology approaches have contributed to, and benefited from, the study of genetic interaction networks. We focus, in particular, on results pertaining to the global multilevel properties of these networks, and the connection between their modular architecture and their functional and evolutionary significance.

Characterization of a new murine endogenous retrovirus-related sequence named MuERVC-C105 is reported. This sequence was found to be most similar to the murine leukemia C-type retroviruses and to murine defective endogenous retrovirus-like families MuRRS and MuRVY, although MuERVC-C105 has a novel LTR. MuERVC-C105, like MuRRS and MuRVY, represents a family of retrovirus-like sequences characterized by many defects in its reading frames. Phylogenetic analyses, in particular analysis of nonsynonymous and synonymous nucleotide substitutions in the descent of these sequences, revealed that the MuERVC-C105, MuRRS, and MuRVY families were each derived from a different nondefective retroviral ancestor, thus justifying the new family name MuERVC. These nondefective ancestors cluster together with Gibbon Ape Leukemia Virus, but were nearly as distinct from each other as are other subgroups of murine leukemia virus (MoMLV, BaEV, GALV). The analysis further indicated that, in spite of the high density of defects in these three families, most of their divergence from their common ancestor was as nondefective retroviruses.